BN0704 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.0946e-05 3.0731e-03
Layer 5 3.0178e-04 1.7700e-03
Layer 6 3.8013e-04 4.6981e-03
Layer 4 3.8039e-04 1.7300e-03
WM 2.2219e-02 9.5936e-02

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SYP Expression Distribution
Gene Specificity Score (GSS)
SYP GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SYP Layer 5 2.8516 0.6934
SNRPN Layer 5 2.5957 0.6773
TUBB2A Layer 5 2.6602 0.6749
RTN1 Layer 5 2.5391 0.6648
STMN2 Layer 5 3.0195 0.6639
TSPYL1 Layer 5 2.5059 0.6630
TOMM7 Layer 4 2.4336 0.6629
YWHAG Layer 5 2.5664 0.6617
RAB3A Layer 5 2.4727 0.6615
SLC17A7 Layer 5 2.6777 0.6580
DNM1 Layer 5 2.6895 0.6569
PKM Layer 4 2.5000 0.6552
BASP1 Layer 5 2.7480 0.6527
NDRG4 Layer 4 2.7598 0.6521
SYT1 Layer 5 2.5059 0.6521
OAZ1 Layer 5 2.3965 0.6513
CALM3 Layer 5 2.4727 0.6498
CHCHD10 Layer 4 2.5723 0.6490
OLFM1 Layer 3 2.9609 0.6477
BEX1 Layer 5 2.7793 0.6472
PRKAR1B Layer 5 2.8594 0.6470
YWHAH Layer 5 2.4395 0.6464
LDHB Layer 5 2.5273 0.6464
UCHL1 Layer 5 2.5215 0.6459
COX6C Layer 3 2.4297 0.6453
RTN3 Layer 5 2.4297 0.6452
BEX3 Layer 5 2.4336 0.6450
ATP5F1B Layer 3 2.5000 0.6449
PGAM1 Layer 5 2.5508 0.6442
UBB Layer 4 2.5781 0.6436
VAMP2 Layer 5 2.4883 0.6432
FBXL16 Layer 5 2.4336 0.6424
ATP6V0C Layer 5 2.3125 0.6424
GNAS Layer 4 2.3242 0.6422
SNCB Layer 5 2.7715 0.6416
EEF1A2 Layer 4 2.6016 0.6416
TPI1 Layer 5 2.4336 0.6406
MTCH1 Layer 5 2.5000 0.6405
VSNL1 Layer 5 2.7188 0.6402
CLSTN1 Layer 4 2.6895 0.6396
CKB Layer 3 2.1387 0.6395
PFN2 Layer 4 2.9805 0.6390
NDUFA4 Layer 4 2.3281 0.6390
HSPA8 Layer 5 2.6016 0.6390
CALY Layer 4 2.7852 0.6374
NEFL Layer 3 2.7480 0.6373
ATP1B1 Layer 5 2.4121 0.6372
STXBP1 Layer 4 2.6895 0.6371
AP2M1 Layer 5 2.5566 0.6364
COX5B Layer 4 2.4336 0.6361

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0704
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0704_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0704/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0704/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0704/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0704/report/PD/BN0704_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0704/report/PD/BN0704_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:21:20
  • Number of Processes: 10
  • Spending Time: 0h 3m